Literature DB >> 25813662

Emergence of coding and its specificity as a physico-informatic problem.

Peter R Wills1, Kay Nieselt, John S McCaskill.   

Abstract

We explore the origin-of-life consequences of the view that biological systems are demarcated from inanimate matter by their possession of referential information, which is processed computationally to control choices of specific physico-chemical events. Cells are cybernetic: they use genetic information in processes of communication and control, subjecting physical events to a system of integrated governance. The genetic code is the most obvious example of how cells use information computationally, but the historical origin of the usefulness of molecular information is not well understood. Genetic coding made information useful because it imposed a modular metric on the evolutionary search and thereby offered a general solution to the problem of finding catalysts of any specificity. We use the term "quasispecies symmetry breaking" to describe the iterated process of self-organisation whereby the alphabets of distinguishable codons and amino acids increased, step by step.

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Year:  2015        PMID: 25813662     DOI: 10.1007/s11084-015-9434-5

Source DB:  PubMed          Journal:  Orig Life Evol Biosph        ISSN: 0169-6149            Impact factor:   1.950


  19 in total

1.  Evolutionary self-organization of cell-free genetic coding.

Authors:  R M Füchslin; J S McCaskill
Journal:  Proc Natl Acad Sci U S A       Date:  2001-07-24       Impact factor: 11.205

Review 2.  On the evolution of structure in aminoacyl-tRNA synthetases.

Authors:  Patrick O'Donoghue; Zaida Luthey-Schulten
Journal:  Microbiol Mol Biol Rev       Date:  2003-12       Impact factor: 11.056

3.  The evolutionary origin of complex features.

Authors:  Richard E Lenski; Charles Ofria; Robert T Pennock; Christoph Adami
Journal:  Nature       Date:  2003-05-08       Impact factor: 49.962

4.  The maintenance of the accuracy of protein synthesis and its relevance to ageing.

Authors:  L E ORGEL
Journal:  Proc Natl Acad Sci U S A       Date:  1963-04       Impact factor: 11.205

5.  On protein synthesis.

Authors:  F H CRICK
Journal:  Symp Soc Exp Biol       Date:  1958

Review 6.  Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life.

Authors:  Nobuto Takeuchi; Paulien Hogeweg
Journal:  Phys Life Rev       Date:  2012-06-13       Impact factor: 11.025

7.  Autocatalytic sets of proteins.

Authors:  S A Kauffman
Journal:  J Theor Biol       Date:  1986-03-07       Impact factor: 2.691

8.  The roots of bioinformatics in theoretical biology.

Authors:  Paulien Hogeweg
Journal:  PLoS Comput Biol       Date:  2011-03-31       Impact factor: 4.475

9.  Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.

Authors:  Gustavo Caetano-Anollés; Minglei Wang; Derek Caetano-Anollés
Journal:  PLoS One       Date:  2013-08-21       Impact factor: 3.240

10.  The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed.

Authors:  Charles W Carter; Li Li; Violetta Weinreb; Martha Collier; Katiria Gonzalez-Rivera; Mariel Jimenez-Rodriguez; Ozgün Erdogan; Brian Kuhlman; Xavier Ambroggio; Tishan Williams; S Niranj Chandrasekharan
Journal:  Biol Direct       Date:  2014-06-14       Impact factor: 4.540

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  6 in total

Review 1.  Experimental solutions to problems defining the origin of codon-directed protein synthesis.

Authors:  Charles W Carter; Peter R Wills
Journal:  Biosystems       Date:  2019-06-06       Impact factor: 1.973

Review 2.  Coding of Class I and II Aminoacyl-tRNA Synthetases.

Authors:  Charles W Carter
Journal:  Adv Exp Med Biol       Date:  2017       Impact factor: 2.622

3.  The Ancient Operational Code is Embedded in the Amino Acid Substitution Matrix and aaRS Phylogenies.

Authors:  Julia A Shore; Barbara R Holland; Jeremy G Sumner; Kay Nieselt; Peter R Wills
Journal:  J Mol Evol       Date:  2019-11-28       Impact factor: 2.395

4.  Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding.

Authors:  Peter R Wills; Charles W Carter
Journal:  Int J Mol Sci       Date:  2020-10-07       Impact factor: 5.923

Review 5.  Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis.

Authors:  Charles W Carter; Peter R Wills
Journal:  Biomolecules       Date:  2021-02-11

6.  Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding.

Authors:  Charles W Carter; Peter R Wills
Journal:  Mol Biol Evol       Date:  2018-02-01       Impact factor: 16.240

  6 in total

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